uBio presentation to Species 2000 May 2004

Universal Biological Indexer and OrganizerResearch Funded by the Andrew W. Mellon Foundation

MBL / WHOI LIBRARY

Universal Biological Indexer and OrganizerResearch Funded by the Andrew W. Mellon Foundation

MBL / WHOI LIBRARY

Universal Biological Indexer and OrganizerResearch Funded by the Andrew W. Mellon Foundation

MBL / WHOI LIBRARY

MBL/WHOI Library

• Stewards of natural history information

• Provide services to our patrons

• Access to information

Universal Biological Indexer and OrganizerResearch Funded by the Andrew W. Mellon Foundation

MBL / WHOI LIBRARY

What information

• Local Data– Special Literature Collections– Specimen databases, herbaria,

sequence data• Remote data

– Journals– ILL– Serial Databases

• (ASFA, JSTOR, etc.)

Universal Biological Indexer and OrganizerResearch Funded by the Andrew W. Mellon Foundation

MBL / WHOI LIBRARY

Information Delivery• Primary access interfaces

– Brute Force - Read it

– Search:

– Browse by hierarchical taxonomic category• Animalia

• Vertebrates• Birds

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Universal Biological Indexer and OrganizerResearch Funded by the Andrew W. Mellon Foundation

MBL / WHOI LIBRARY

Problem: Multiple Names• Common names• Scientific Names• N:N• Persistent • Pervasive

– Pectinaria gouldii– Cistenides gouldii

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Universal Biological Indexer and OrganizerResearch Funded by the Andrew W. Mellon Foundation

MBL / WHOI LIBRARY

Problem: Multiple categories

• No taxonomic opinion• Patron opinions are what counts• Multiple basis for derivation• Dynamic• Require any/all

ITISAnimaliaChordataOsteichthysActinopterygiiPerciformesPomatomidaePomatomussaltatrix

NCBIEukaryotaFungi/Metazoa groupMetazoaEumetazoaBilateriaCoelomataDeuterostomiaChordataCraniataVertebrataGnathostomataTeleostomiEuteleostomiActinopterygiiActinopteriNeopterygiiTeleosteiElopocephalaClupeocephalaEuteleosteiNeognathiNeoteleosteiEurypterygiiCtenosquamataAcanthomorphaEuacanthomorphaHolacanthopterygiiAcanthopterygiiEuacanthopterygiiPercomorphaPerciformesPercoideiPomatomidaePomatomussaltatrix

Universal Biological Indexer and OrganizerResearch Funded by the Andrew W. Mellon Foundation

MBL / WHOI LIBRARY

Generalized Solution

• Ad-hoc Fix• Systematic Fix• Network thesaurus• “Plug” in applications• Any name• Any classification

Universal Biological Indexer and OrganizerResearch Funded by the Andrew W. Mellon Foundation

MBL / WHOI LIBRARY

What it should do

• Account for any “name” relevant to the defined “community”

• Provides taxonomic metadata to biological information providers– Libraries– Publishers

• Provides detailed accounting of usage of taxonomic metadata to contributors of knowledge

Universal Biological Indexer and OrganizerResearch Funded by the Andrew W. Mellon Foundation

MBL / WHOI LIBRARY

WHY do we want a solution

• Increase access to biological information assets• Too much information is inaccessible

• It should directly benefit contributors of knowledge

• Directly link usage to attribution

Universal Biological Indexer and OrganizerResearch Funded by the Andrew W. Mellon Foundation

MBL / WHOI LIBRARY

Increase Access: How?

• Supplement name information that is available for searching and matching name strings – (Example)– Vernacular, homotypic, heterotypic

• Provide hierarchical structures for browsing large biological data collections– (Example)

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Universal Biological Indexer and OrganizerResearch Funded by the Andrew W. Mellon Foundation

MBL / WHOI LIBRARY

What we came up with:uBio• Database of taxonomic metadata (TNS)• Network Service (SOAP)• Workgroup management system

• Intent: – Demonstrate a need through pilot system– Add enough names to show that the system works at scale– Look for partners who can curate names

Universal Biological Indexer and OrganizerResearch Funded by the Andrew W. Mellon Foundation

MBL / WHOI LIBRARY

TNS

Universal Biological Indexer and OrganizerResearch Funded by the Andrew W. Mellon Foundation

MBL / WHOI LIBRARY

TNS: NameBank• Nomenclature -

– Scientific -> basionym– Vernacular -> scientific

• Objective Relationships– Vernacular mappings based on associations– Homotypic– Lexical variants– Management Classification

• No name left behind

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Universal Biological Indexer and OrganizerResearch Funded by the Andrew W. Mellon Foundation

MBL / WHOI LIBRARY

TNS: ClassificationBank

• Subjective• Hierarchies• Synonymies• Varying degrees of granularity

– Checklists (-Example)– Junior Synonyms (-Example)– Full bibliographic review (-Example) QuickTime™ and aTIFF (Uncompressed) decompressorare needed to see this picture.

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Universal Biological Indexer and OrganizerResearch Funded by the Andrew W. Mellon Foundation

MBL / WHOI LIBRARY

TNS: Accounting• Multiple sources may be responsible for a single

data object• Any data change is linked to a source• Links all TNS data to a contributing Agent

– NameBank/ClassificationBank specific– Each interacts with it independently– (Example)

• Names belong to sourcesQuickTime™ and aTIFF (Uncompressed) decompressorare needed to see this picture.

Universal Biological Indexer and OrganizerResearch Funded by the Andrew W. Mellon Foundation

MBL / WHOI LIBRARY

Network Service: Methods

• SOAP– http-based

• Four primary methods– nameBank_search (locate factual instance of name)– nameBank_object (objective metadata)– classificationBank_search (locate interpretations of name)– classificationBank__object (subjective metadata)– …more to come

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Universal Biological Indexer and OrganizerResearch Funded by the Andrew W. Mellon Foundation

MBL / WHOI LIBRARY

Network Service :Attribution

• Every datum sent out via service is logged– nameBankID– datestamp– Client IP– Calling method– requestorIP

• <client optional>

Universal Biological Indexer and OrganizerResearch Funded by the Andrew W. Mellon Foundation

MBL / WHOI LIBRARY

Log is Processed

• Network service <-> Contributing Agent– By date– By IP– By method– Full Accounting of usage

• Intent is to be a proxy for these data

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Universal Biological Indexer and OrganizerResearch Funded by the Andrew W. Mellon Foundation

MBL / WHOI LIBRARY

Why

• Increase utility– Put data to work in multiple ways

• Increase value– When benefits are clear

• Increase support for it– We can garner support from these communities

Universal Biological Indexer and OrganizerResearch Funded by the Andrew W. Mellon Foundation

MBL / WHOI LIBRARY

Workgroup Management System

PlatypusNetworkedMulti-platformMultiple UsersEase management burdenInput parser

Universal Biological Indexer and OrganizerResearch Funded by the Andrew W. Mellon Foundation

MBL / WHOI LIBRARY

Collaborate

• Reduce duplication of effort• Maximize accountability to those that DO the work• Utilize funding resources for new work• New uses for existing work

Universal Biological Indexer and OrganizerResearch Funded by the Andrew W. Mellon Foundation

MBL / WHOI LIBRARY

Multiple Initiatives

• Range of focus• Different priorities• Different scales• Multiple opinions

• Yet there is common data• Any name in list is useful to all

Universal Biological Indexer and OrganizerResearch Funded by the Andrew W. Mellon Foundation

MBL / WHOI LIBRARY

Layered Systems Work

Universal Biological Indexer and OrganizerResearch Funded by the Andrew W. Mellon Foundation

MBL / WHOI LIBRARY

Encapsulate: NameBank

• Nomenclature reference core

• Independent from any specific application/system

• Maintain full attribution to source and edits

• Makes our TNS portable

• Collaborative foundation

Universal Biological Indexer and OrganizerResearch Funded by the Andrew W. Mellon Foundation

MBL / WHOI LIBRARY

Federate

• Layered architecture• Common Foundation• Multiple Directions• Interchange• Cooperation

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Universal Biological Indexer and OrganizerResearch Funded by the Andrew W. Mellon Foundation

MBL / WHOI LIBRARY

Domain Layer

Universal Biological Indexer and OrganizerResearch Funded by the Andrew W. Mellon Foundation

MBL / WHOI LIBRARY

Next

• Formalize the NameBank split from TNS• Empty it and start over

– uBio is only a prototype• Look for taxonomic partners• Focus on solutions for libraries• Bring library community to partnership